AiPD: Autoinhibited Protein Database

P09661

Gene name	SNRPA1
Protein name	U2 small nuclear ribonucleoprotein A'
Names	U2 snRNP A'
Species	Homo sapiens (Human)
KEGG Pathway	hsa:6627
EC number
Protein Class

Descriptions

The autoinhibited protein was predicted that may have potential autoinhibitory elements via cis-regPred.

Autoinhibitory domains (AIDs)

140-255 (Predicted disordered autoinhibitory region) PR

Target domain
Relief mechanism
Assay	cis-regPred

AID

140-255 (Predicted disordered autoinhibitory region)

Target domain

Relief mechanism

Assay

cis-regPred

Accessory elements

No accessory elements

References

Yeon JH et al. (2016) "Systems-wide Identification of cis-Regulatory Elements in Proteins", Cell Systems, 2, 89-100

Autoinhibited structure

Activated structure

31 structures for P09661

Entry ID	Method	Resolution	Chain	Position	Source
1A9N	X-ray	238 A	A/C	1-176	PDB
5MQF	EM	590 A	W	1-255	PDB
5O9Z	EM	450 A	z	1-255	PDB
5XJC	EM	360 A	o	1-255	PDB
5YZG	EM	410 A	o	1-255	PDB
5Z56	EM	510 A	o	1-255	PDB
5Z57	EM	650 A	o	1-255	PDB
5Z58	EM	490 A	o	1-255	PDB
6AH0	EM	570 A	o	1-255	PDB
6AHD	EM	380 A	o	1-255	PDB
6FF7	EM	450 A	W	1-255	PDB
6ICZ	EM	300 A	o	1-255	PDB
6ID0	EM	290 A	o	1-255	PDB
6ID1	EM	286 A	o	1-255	PDB
6QDV	EM	330 A	W	2-162	PDB
6QX9	EM	328 A	2A	1-255	PDB
6Y53	EM	710 A	a	1-255	PDB
6Y5Q	EM	710 A	a	1-255	PDB
7A5P	EM	500 A	W	1-255	PDB
7ABG	EM	780 A	W	1-255	PDB
7ABI	EM	800 A	W	1-255	PDB
7EVO	EM	250 A	F	1-255	PDB
7VPX	EM	300 A	F	1-255	PDB
7W59	EM	360 A	o	1-255	PDB
7W5A	EM	360 A	o	1-255	PDB
7W5B	EM	430 A	o	1-255	PDB
8C6J	EM	280 A	W	1-255	PDB
8CH6	EM	590 A	r	1-255	PDB
8HK1	EM	270 A	F	1-255	PDB
8QO9	EM	529 A	2A	1-255	PDB
AF-P09661-F1	Predicted				AlphaFoldDB

144 variants for P09661

Variant ID(s)	Position	Change	Description	Diseaes Association	Provenance
TCGA novel	1	M>?	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA7763347 rs777988186	4	L>M		No	ClinGen ExAC TOPMed gnomAD
rs1404929833 CA393967197	5	T>A		No	ClinGen TOPMed gnomAD
rs772555366 CA7763346	5	T>M		No	ClinGen ExAC TOPMed gnomAD
CA393967167 rs1390475867	10	E>K		No	ClinGen TOPMed
CA276343375 rs561721413 CA7763344	11	Q>H		No	ClinGen 1000Genomes ExAC TOPMed gnomAD
rs1040869856 CA276343370	13	A>V		No	ClinGen TOPMed gnomAD
CA7763343 rs755005074	14	Q>R		No	ClinGen ExAC gnomAD
rs1243664450 CA393967133	15	Y>H		No	ClinGen TOPMed
rs1447146268 CA393967126	16	T>A		No	ClinGen gnomAD
rs1314344421 CA393967118	17	N>S		No	ClinGen TOPMed
CA7763342 rs753952520	20	R>H		No	ClinGen ExAC gnomAD
CA7763341 rs781038951	21	D>Y		No	ClinGen ExAC gnomAD
CA7763340 rs757152353	22	R>W		No	ClinGen ExAC TOPMed gnomAD
CA393967072 rs1400924250	25	D>N	Variant assessed as Somatic; impact. [NCI-TCGA]	No	ClinGen NCI-TCGA gnomAD
CA7763338 rs763788242	26	L>F		No	ClinGen ExAC gnomAD
rs754665870 CA7763314	28	G>E		No	ClinGen ExAC
rs905473905 CA276343248	28	G>R		No	ClinGen TOPMed
rs1226462085 CA393967034	29	Y>C		No	ClinGen gnomAD
rs1272146544 CA393967037	29	Y>H		No	ClinGen gnomAD
TCGA novel	30	K>N	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs138801817 CA7763311	32	P>S		No	ClinGen 1000Genomes ESP ExAC TOPMed gnomAD
rs755270186 CA276340915	33	V>I		No	ClinGen TOPMed gnomAD
CA393966990 rs1443545247	36	N>H		No	ClinGen gnomAD
rs749503765 CA7763305	40	T>K		No	ClinGen ExAC gnomAD
rs749503765 CA7763306	40	T>M		No	ClinGen ExAC gnomAD
rs143051052 CA276340882	47	I>V		No	ClinGen ESP TOPMed gnomAD
CA7763301 rs557125509	51	D>E		No	ClinGen 1000Genomes ExAC TOPMed gnomAD
rs1421616242 CA393966888	51	D>N		No	ClinGen gnomAD
CA393966883 rs1404755444	51	D>V		No	ClinGen TOPMed gnomAD
rs138420806 CA7763300	53	E>D		No	ClinGen ESP ExAC TOPMed gnomAD
rs947423040 CA276340853	58	D>N		No	ClinGen TOPMed
rs1490445110 CA393966830	59	G>D		No	ClinGen gnomAD
CA7763299 rs748156963	59	G>S		No	ClinGen ExAC gnomAD
TCGA novel	60	F>V	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
TCGA novel	61	P>L	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA276340847 rs1053301275	63	L>S		No	ClinGen TOPMed gnomAD
CA7763298 rs778848364	64	R>K		No	ClinGen ExAC gnomAD
rs753518771 CA7763296	66	L>P		No	ClinGen ExAC gnomAD
rs1438341100 CA393966778	67	K>R		No	ClinGen TOPMed
CA393966751 rs1157834138	71	V>A		No	ClinGen gnomAD
CA393966741 rs1286980212	73	N>H		No	ClinGen gnomAD
CA393966738 rs1409644499	73	N>S		No	ClinGen gnomAD
TCGA novel	75	R>N	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA7763295 rs766082491	75	R>T		No	ClinGen ExAC gnomAD
rs755543547 CA7763294	76	I>L		No	ClinGen ExAC gnomAD
CA7763284 rs745867854	78	R>C	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ExAC NCI-TCGA gnomAD
rs776784734 CA7763283	78	R>H	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ExAC NCI-TCGA gnomAD
rs745867854 CA393980516	78	R>S		No	ClinGen ExAC gnomAD
TCGA novel	81	E>V	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
TCGA novel	82	G>R	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA276391133 rs768641217	83	L>V		No	ClinGen Ensembl
rs1271985821 CA393980451	88	P>S		No	ClinGen TOPMed
rs1207067390 CA393980439	90	L>V		No	ClinGen TOPMed
rs749129281 CA7763278	94	I>F		No	ClinGen ExAC gnomAD
rs1243754804 CA393980392	97	N>S		No	ClinGen gnomAD
rs142731245 CA7763275	99	S>N		No	ClinGen 1000Genomes ESP ExAC TOPMed gnomAD
rs114919170 CA7763273	100	L>I		No	ClinGen 1000Genomes ExAC TOPMed gnomAD
rs114919170 CA7763274	100	L>V		No	ClinGen 1000Genomes ExAC TOPMed gnomAD
rs369821067 CA393980366	101	V>L		No	ClinGen ESP ExAC TOPMed gnomAD
CA7763271 rs369821067	101	V>M	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ESP ExAC NCI-TCGA TOPMed gnomAD
CA7763242 rs769605360	108	P>L		No	ClinGen ExAC gnomAD
CA7763243 rs775327517	108	P>S		No	ClinGen ExAC TOPMed gnomAD
CA7763241 rs745669436	112	L>V		No	ClinGen ExAC TOPMed gnomAD
CA7763240 rs577233883	114	S>L		No	ClinGen 1000Genomes ExAC TOPMed gnomAD
rs1244018389 CA393979883	118	L>V		No	ClinGen gnomAD
TCGA novel	119	S>C	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA393979769 rs1305290777	122	R>G		No	ClinGen gnomAD
rs772901598 CA7763219	124	P>A		No	ClinGen ExAC gnomAD
CA393979702 rs1276985340	125	V>A		No	ClinGen gnomAD
CA7763217 rs747643637	125	V>I		No	ClinGen ExAC gnomAD
CA7763216 rs779411044	126	T>I		No	ClinGen ExAC
rs755457351 CA7763215	127	N>S		No	ClinGen ExAC TOPMed gnomAD
rs749866603 CA7763214	129	K>Q		No	ClinGen ExAC gnomAD
rs780565103 CA7763213	130	H>Q		No	ClinGen ExAC gnomAD
CA393979591 rs1479198702	130	H>R		No	ClinGen gnomAD
rs1400280744 CA393979582	131	Y>D		No	ClinGen TOPMed gnomAD
CA393979511 rs1464999709	133	L>W		No	ClinGen gnomAD
rs1255731640 CA393979466	135	V>A		No	ClinGen TOPMed
rs756583632 CA7763212	136	I>T		No	ClinGen ExAC gnomAD
CA393979462 rs1249280480	136	I>V		No	ClinGen gnomAD
CA393979420 rs1446316109	138	K>E		No	ClinGen gnomAD
rs757317130 CA7763209	140	P>L		No	ClinGen ExAC gnomAD
rs767869756 CA7763210	140	P>S		No	ClinGen ExAC gnomAD
rs767869756 CA7763211	140	P>T		No	ClinGen ExAC gnomAD
CA393979347 rs1596470717	142	V>I		No	ClinGen Ensembl
rs1233769122 CA393979336	143	R>G		No	ClinGen gnomAD
TCGA novel	148	Q>H	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA276385869 rs908504284	151	K>Q		No	ClinGen Ensembl
CA7763192 rs150710048	155	R>H	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen 1000Genomes ExAC NCI-TCGA TOPMed gnomAD
rs1316539546 CA393978396	158	A>S		No	ClinGen Ensembl
rs1459858540 CA393978376	160	K>N		No	ClinGen gnomAD
CA7763191 rs781405747	161	M>I		No	ClinGen ExAC gnomAD
rs1476596171 CA393978370	161	M>T		No	ClinGen TOPMed
rs1166981227 CA393978350	164	G>S		No	ClinGen TOPMed
TCGA novel	165	K>N	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA393978335 rs1166299700	166	R>W		No	ClinGen gnomAD
CA393978291 rs1427468833	173	D>N		No	ClinGen gnomAD
rs1413812521 CA393978279	174	I>T		No	ClinGen gnomAD
CA276385184 rs967280716	175	A>T		No	ClinGen TOPMed
CA393978262 rs1396580511	177	R>K		No	ClinGen TOPMed
rs150109462 CA276385157	180	T>I		No	ClinGen ESP TOPMed gnomAD
rs186863613 CA7763161	182	N>S		No	ClinGen 1000Genomes ExAC TOPMed gnomAD
rs1002602341 CA276384705	183	P>L		No	ClinGen TOPMed
rs761721002 CA393978201	184	G>A		No	ClinGen ExAC gnomAD
CA7763160 rs761721002	184	G>D		No	ClinGen ExAC gnomAD
rs527750619 CA393978189	186	G>A		No	ClinGen 1000Genomes ExAC TOPMed gnomAD
rs527750619 CA7763159	186	G>V		No	ClinGen 1000Genomes ExAC TOPMed gnomAD
rs763834626 CA7763158	187	L>F		No	ClinGen ExAC gnomAD
CA276384698 rs866869396	188	P>S		No	ClinGen gnomAD
rs531907281 CA7763157 COSM959677	189	T>A	endometrium [Cosmic]	No	ClinGen cosmic curated ExAC TOPMed gnomAD
CA7763153 rs142009828	195	G>A		No	ClinGen ESP ExAC TOPMed gnomAD
CA393978131 rs142009828	195	G>E		No	ClinGen ESP ExAC TOPMed gnomAD
TCGA novel	196	P>S	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs1426191744 CA393978129	196	P>T		No	ClinGen gnomAD
CA7763150 COSM1708589 rs773240837	197	S>F	skin [Cosmic]	No	ClinGen cosmic curated ExAC gnomAD
CA7763149 rs772297229	198	P>S	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ExAC NCI-TCGA gnomAD
CA7763147 rs147560644	200	D>E		No	ClinGen ESP ExAC TOPMed gnomAD
TCGA novel	200	D>G	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA7763148 rs748428177	200	D>N		No	ClinGen ExAC gnomAD
CA393978100 rs1474091788	201	V>I		No	ClinGen TOPMed
CA393978082 rs1418348854	203	A>V		No	ClinGen TOPMed
CA7763123 rs780921357	208	I>V		No	ClinGen ExAC gnomAD
CA276383963 rs755978201	209	A>T		No	ClinGen Ensembl
rs1231250957 CA393978016	211	A>V		No	ClinGen TOPMed
rs1396477329 CA393977998	215	A>T		No	ClinGen gnomAD
CA393977995 rs1381110043	215	A>V		No	ClinGen gnomAD
CA393977977 rs1375110306	218	E>K		No	ClinGen gnomAD
CA276383958 rs943781712	219	R>K		No	ClinGen Ensembl
rs1463642202 CA393977951	222	G>R		No	ClinGen gnomAD
TCGA novel	224	L>A	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA7763118 rs752376277	226	S>A		No	ClinGen ExAC TOPMed gnomAD
rs1567124067 CA393977890	231	G>D		No	ClinGen Ensembl
CA7763117 rs373922948	233	E>G		No	ClinGen ESP ExAC TOPMed gnomAD
rs1258736102 CA393977873	233	E>K		No	ClinGen TOPMed
CA7763116 rs145302917	234	R>C	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ESP ExAC NCI-TCGA gnomAD
rs753401813 CA7763115	234	R>H		No	ClinGen ExAC TOPMed gnomAD
rs1567122671 CA393977173	243	E>K		No	ClinGen Ensembl
CA7763094 rs141391407	244	E>D		No	ClinGen 1000Genomes ESP ExAC TOPMed gnomAD
rs991548658 CA276380484	247	E>Q		No	ClinGen TOPMed gnomAD
rs762095184 CA7763093	249	D>G		No	ClinGen ExAC TOPMed gnomAD
CA393977081 rs1413188935	250	T>K		No	ClinGen gnomAD
CA7763092 rs751930111	252	T>I		No	ClinGen ExAC gnomAD
CA393977043 rs1473049355	254	G>R		No	ClinGen Ensembl

No associated diseases with P09661

2 regional properties for P09661

Type	Name	Position	InterPro Accession
repeat	Leucine-rich repeat	89 - 110	IPR001611
domain	U2A'/phosphoprotein 32 family A, C-terminal	128 - 146	IPR003603

Functions

		Description
EC Number
Subcellular Localization	Nucleus
PANTHER Family
PANTHER Subfamily
PANTHER Protein Class
PANTHER Pathway Category	No pathway information available

10 GO annotations of cellular component

Name	Definition
catalytic step 2 spliceosome	A spliceosomal complex that contains three snRNPs, including U5, bound to a splicing intermediate in which the first catalytic cleavage of the 5' splice site has occurred. The precise subunit composition differs significantly from that of the catalytic step 1, or activated, spliceosome, and includes many proteins in addition to those found in the associated snRNPs.
nuclear body	Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
nuclear speck	A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
small nuclear ribonucleoprotein complex	A ribonucleoprotein complex that contains at least one RNA of the small nuclear RNA (snRNA) class and as well as its associated proteins. These are typically named after the snRNA(s) they contain, e.g. U1 snRNP, U4/U6 snRNP, or 7SK snRNP. Many, of these complexes become part of the spliceosome involved in splicing of nuclear mRNAs. Others are involved in regulation of transcription elongation or 3'-end processing of replication-dependent histone pre-mRNAs.
spliceosomal complex	Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.
U2 snRNP	A ribonucleoprotein complex that contains small nuclear RNA U2, a heptameric ring of Sm proteins, as well as several proteins that are unique to the U2 snRNP, most of which remain associated with the U2 snRNA both while the U2 snRNP is free or assembled into a series of spliceosomal complexes.
U2-type catalytic step 2 spliceosome	A spliceosomal complex that contains the U2, U5 and U6 snRNPs bound to a splicing intermediate in which the first catalytic cleavage of the 5' splice site has occurred. The precise subunit composition differs significantly from that of the catalytic step 1, or activated, spliceosome, and includes many proteins in addition to those found in the U2, U5 and U6 snRNPs.
U2-type precatalytic spliceosome	A spliceosomal complex that is formed by the recruitment of the preassembled U4/U6.U5 tri-snRNP to the prespliceosome. Although all 5 snRNPs are present, the precatalytic spliceosome is catalytically inactive. The precatalytic spliceosome includes many proteins in addition to those found in the U1, U2 and U4/U6.U5 snRNPs.

2 GO annotations of molecular function

Name	Definition
RNA binding	Binding to an RNA molecule or a portion thereof.
U2 snRNA binding	Binding to a U2 small nuclear RNA (U2 snRNA).

4 GO annotations of biological process

Name	Definition
mRNA splicing, via spliceosome	The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
RNA splicing	The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
spermatogenesis	The developmental process by which male germ line stem cells self renew or give rise to successive cell types resulting in the development of a spermatozoa.
U2-type prespliceosome assembly	The aggregation, arrangement and bonding together of a set of components to form an U2-type prespliceosome.

2 homologous proteins in AiPD

UniProt AC	Gene Name	Protein Name	Species	Evidence Code
P57784	Snrpa1	U2 small nuclear ribonucleoprotein A'	Mus musculus (Mouse)	PR
P43333	At1g09760	U2 small nuclear ribonucleoprotein A'	Arabidopsis thaliana (Mouse-ear cress)	PR

10	20	30	40	50	60
MVKLTAELIE	QAAQYTNAVR	DRELDLRGYK	IPVIENLGAT	LDQFDAIDFS	DNEIRKLDGF
70	80	90	100	110	120
PLLRRLKTLL	VNNNRICRIG	EGLDQALPCL	TELILTNNSL	VELGDLDPLA	SLKSLTYLSI
130	140	150	160	170	180
LRNPVTNKKH	YRLYVIYKVP	QVRVLDFQKV	KLKERQEAEK	MFKGKRGAQL	AKDIARRSKT
190	200	210	220	230	240
FNPGAGLPTD	KKKGGPSPGD	VEAIKNAIAN	ASTLAEVERL	KGLLQSGQIP	GRERRSGPTD
250
DGEEEMEEDT	VTNGS